Chop the chipotle pepper, and onion then add it to a bowl with the 1/4 of the spice rub and the beer and vinegar to make a marinade.
Pour the marinade over the brisket and marinade overnight
Drain marinade and pat the brisket down. Put the brisket in a heavy roasting pan and pat 3/4 remaining rub over the brisket.
Place in a 300 degree F oven for about 2 hours.
Sprinkle with the remaining rub and cover with foil. Cook for 1-2 more hours minimum or until tender.